Detecting Darwinian Shortfalls in the Amazonian Odonata.

Among the oldest winged insects, odonates are a monophyletic order that have become important models for ecological studies because of their highly diverse reproductive behaviors and their role as top predators and bioindicators. However, knowledge on evolutionary relationships within the order is still scarce compared to other taxa, and this situation is even more complicated in areas with high biodiversity, such as in the Amazon. Here, we sought to identify knowledge gaps on Amazonian Odonata regarding three main aspects: (i) how the inclusion of Amazonian taxa affects our interpretation of the evolutionary relationships of Zygoptera and Anisoptera; (ii) the position of Amazonian taxa in the existing supertree of the Odonata; (iii) dating evolutionary divergence between nodes using fossil records; (iv) assessing whether more species-rich basins (e.g., Amazon basin) have a larger phylogenetic gap when compared to basins with lower richness in South and Central America; and (v) in the light of our knowledge, we discuss diversification patterns found in the most predominant clades of Amazonian taxa. We built a supertree from currently available phylogenetic information of Odonata. The results show that there is no genetic information for 85% (n: 503) of the Amazonian species and that family level relationships are unknown for 17 genera. After compiling the data, we observed that clades belonging to Neotropical lineages are the most poorly resolved, with large polytomies. This problem was identified in many Anisoptera genera, such as Macrothemis, Dasythemis, Elasmothemis, and Erythrodiplax. Our results also suggest that not always the richest basins have the greatest phylogenetic gaps. As expected, we found important gaps in the existing Odonata phylogenies, especially in clades that include Amazonian representatives, that are also those less known from ecological and conservation perspectives.

Phylogenetic uncertainty and the inference of patterns in community ecology and comparative studies.

Progress in phylogenetic community ecology is often limited by the availability of phylogenetic information and the lack of appropriate methods and solutions to deal with this problem. We estimate the effect of the lack of phylogenetic information on the relations among taxa measured by commonly used phylogenetic metrics in comparative studies and community ecology, namely: Blomberg's K phylogenetic signal, Faith's Phylogenetic Diversity (PD), Mean Phylogenetic Distance (MPD) and Mean Nearest Taxon Distance (MNTD). To overcome this problem, we tested two possible solutions: Polytomic trees and Operational trees. Our results show that the effects on K values strongly depended on the level of phylogenetic signal. In the case of the community metrics, the effects were insensitive to the patterns of species distribution in the communities. Community metrics tended to be overestimated with both Polytomic and Operational trees, but the overestimation was higher with Polytomic trees. PD and MPD metrics were less biased than MNTD metric. We show that the lack of phylogenetic resolution is not necessarily problematic for all analyses and that its effect will depend on the chosen metric and on the solutions used to deal with the problem. Based on our results, we suggest that ecologists should prefer the Operational tree solution to remove polytomies in the phylogenetic tree and take careful consideration while designing experiments, and analyzing and interpreting the results of phylogenetic metrics.

Nuevos marcadores mitocondriales mejoran la filogenia de la tortuga carey Eretmochelys imbricata (Testudines: Cheloniidae) / New mitochondrial markers improve the phylogeny of the hawksbill turtle Eretmochelys imbricata (Testudines: Cheloniidae)

Las tortugas marinas (Cheloniidae) son un grupo de siete especies originadas en el cretaceo. Analisis de secuencias parciales de DNA mitocondrial han revelado inconsistencias filogeneticas dentro de este grupo de quelonios. Sin embargo, estos marcadores mitocondriales han permitido entender y dilucidar la composicion de las poblaciones en areas de forrajeo, habitos reproductivos, inferencias de patrones de migracion y tambien definir las unidades de manejo en el mundo, con el fin de proponer planes de manejo y conservacion. El objetivo de este estudio fue evaluar la posicion de la tortuga carey E. imbricata dentro de la familia Cheloniidae y la filogenia de las tortugas marinas utilizando genes mitocondriales codificantes de proteinas, genes ribosomicos y el genoma mitocondrial completo de la tortuga carey anidante del Caribe colombiano, al compararlo con las otras seis especies de tortugas marinas disponibles en GenBank. Se utilizaron cuatro metodos de inferencias filogeneticas: Neighbor-Joining (NJ), Maxima Verosimilitud (ML), Maxima Parsimonia (MP) e Inferencia Bayesiana (IB). Los arboles NJ, ML, MP e IB mostraron que ND2, COX1, 16S ARNr, ND5, 12S ARNr, ND4, COX3 y ND1 son los marcadores que presentan una mejor resolucion filogenetica con sustentos bootstrap entre 89,0% y 99,98%. Los genes ATP6, ATP8, COX2, ND3, ND4L y ND5 presentaron politomias y establecieron relaciones filogeneticas equivocadas. El analisis con el mitogenoma completo presento arboles altamente sustentados (bootstrap de 98,0%) en comparacion con el analisis con marcadores individuales. Los arboles obtenidos con el gen ND2 e IB resolvieron con buen sustento las relaciones evolutivas entre las especies comparadas, consolidandose la posicion de E. imbricata dentro de la tribu Carettini con probabilidad posterior de 0,98-1,0. Los marcadores ND2, ND5, ND4, COX3 y ND1 no han sido utilizados en trabajos previos y representan una nueva alternativa para explicar la filogenia en este grupo de reptiles marinos. En el presente caso utilizando mitogenomas completos se obtuvieron arboles robustos y altamente sustentados.

The sea turtles (Cheloniidae) are a group of seven species of cretaceous origin. Analyses of partial mitochondrial sequences have revealed phylogenetic inconsistences within this group. Nevertheless, these mitochondrial markers have allowed us to understand, explain and clarify population composition in areas of foraging, reproductive habits, inferences of migration patterns and, also, to define management units in the world, in order to trace conservation and monitoring plans. In this study, four methods were evaluated and compared for phylogenetic inference (Neighbor-Joining-NJ, Maximum Likelihood-ML, Maximum Parsimony-MP and Bayesian inference-BI) by using coding genes, ribosomal genes and full mitogenomes of the hawksbill, E. imbricata, and other six species of sea turtles obtained from GenBank. The sequences were analyzed independently and jointly to identify the method and marker that better explain the phylogenetic relationships among this group of reptiles. The NJ, ML, MP and BI trees showed that ND2, COX1, 16S rRNA, ND5, 12S rRNA, ND4 and COX3 are the markers that give phylogenetic trees with better resolution and support, with bootstrap values ranging from 89.0% to 99.98%. ATP6, ATP8, COX2, ND1, ND3, ND5 and ND4L genes presented polytomies. The analysis with full mitogenome often provides highly supported trees (bootstrap 98.0%) compared with single marker analysis. Trees obtained with the BI method and the ND2 gene is the one that better resolved the evolutionary relationships among the species, consolidating the position of E. imbricata within the Carettini tribe with a value of posterior probability of 0.98-1.0. The markers ND2, ND4, ND5 and COIII, not used in previous works, represent a new alternative to explain the phylogeny in this group of marine reptiles. In the present study, a complete mitogenome analysis produced robust and highly supported trees.

Discriminating the effects of phylogenetic hypothesis, tree resolution and clade age estimates on phylogenetic signal measurements.

Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure.